NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1348538 Query DataSets for GSM1348538
Status Public on Jul 10, 2014
Title H2Bub1 JQ1 E2 rep3
Sample type SRA
 
Source name MCF7 breast cancer cells
Organism Homo sapiens
Characteristics cell type: Human breast adenocarcinoma
cell line: MCF7
passages: 20-30
chip-seq antibody: H2Bub1 D11 (5546 from Cell signaling, 1.5 µL used)
Treatment protocol After 2 days of hormone deprivation, MCF7 cells were treated with 30 minutes of 150 nM JQ1 treatment prior to 10 nmol/L 17-β-estradiol (Sigma-Aldrich) treatment for 2 hours. DMSO and vehicle were added as negative controls.
Growth protocol MCF7 cells were grown in phenol red- free high-glucose Dulbecco's Modified Eagle's Media (DMEM; Invitrogen) with 10% bovine growth serum (Thermo Scientific). For estrogen induction experiments, after one day of cell-splitting, the media was changed to DMEM containing 5% charcoal-dextran treated FBS (Sigma).
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked with 1% Formaldehyde for 10 or 20 minutes and quenched with 125 mM Glycine. The nuclear pellets were sonicated to the fragment range of 200-400 bp. Sonicated extracts were incubated with specific antibodies at 4˚C overnight and ChIP-immune complexes were pulled down using Protein A sepharose.
Library preparations were done using NEBnext Ultra DNA library preparation kit according to the manufacturer’s instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description Cells were crosslinked with 1 % formaldehyde for 10 minutes.
Data processing The reads were mapped to the human reference genome (UCSC HG19) using Bowtie (version 1.0.0) (Langmead et al., 2009).
Peak-calling was done by Model based analysis of ChIP-seq (MACS version 1.4.2) (Zhang et al., 2008).
Coverage was normalized on the total number of mapped reads per hundred million.
Genome_build: hg19
Supplementary_files_format_and_content: WIG, normalized
 
Submission date Mar 14, 2014
Last update date May 15, 2019
Contact name Steven A Johnsen
E-mail(s) sjohnsen@alumni.mayo.edu
Organization name University Medical Center Göttingen
Department Department of General, Visceral and Pediatric Surgery
Street address Robert-Koch-Straße 40
City Göttingen
State/province Niedersachsen
ZIP/Postal code 37075
Country Germany
 
Platform ID GPL16791
Series (2)
GSE55921 Bromodomain protein BRD4 is required for estrogen receptor-dependent transcription and enhancer activation [ChIP-seq]
GSE55923 Bromodomain protein BRD4 is required for estrogen receptor-dependent transcription and enhancer activation
Relations
BioSample SAMN02689287
SRA SRX490449

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap